7ZSB image
Deposition Date 2022-05-06
Release Date 2022-11-16
Last Version Date 2025-07-02
Entry Detail
PDB ID:
7ZSB
Keywords:
TRANSCRIPTION
Title:
Yeast RNA polymerase II transcription pre-initiation complex with the +1 nucleosome and NTP, complex C
Biological Source:
Source Organism:
Saccharomyces cerevisiae (Taxon ID: 4932)
Xenopus laevis (Taxon ID: 8355)
synthetic construct (Taxon ID: 32630)
Host Organism:
Saccharomyces cerevisiae
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
6.60 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7ZSB validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA repair factor IIH helicase subunit XPD
Gene (Uniprot):RAD3
Chain IDs:W (auth: 0)
Chain Length:778
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P06839 Pfam ID:PF06733, PF06777, PF13307
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA repair factor IIH subunit TFB1
Gene (Uniprot):TFB1
Chain IDs:X (auth: 1)
Chain Length:645
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32776 Pfam ID:PF08567, PF03909
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA repair factor IIH subunit TFB2
Gene (Uniprot):TFB2
Chain IDs:Y (auth: 2)
Chain Length:517
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q02939 Pfam ID:PF03849, PF18307
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II transcription factor B subunit 3
Gene (Uniprot):TFB3
Chain IDs:Z (auth: 3)
Chain Length:324
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q03290 Pfam ID:PF17121, PF06391
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA repair factor IIH subunit TFB4
Gene (Uniprot):TFB4
Chain IDs:AA (auth: 4)
Chain Length:341
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q12004 Pfam ID:PF03850
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA repair factor IIH subunit TFB5
Gene (Uniprot):TFB5
Chain IDs:BA (auth: 5)
Chain Length:76
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q3E7C1 Pfam ID:PF06331
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA repair factor IIH subunit SSL1
Gene (Uniprot):SSL1
Chain IDs:CA (auth: 6)
Chain Length:464
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q04673 Pfam ID:PF04056, PF07975
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription and DNA repair factor IIH helicase subunit XPB
Gene (Uniprot):SSL2
Chain IDs:DA (auth: 7)
Chain Length:843
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q00578 Pfam ID:PF13625, PF04851, PF16203
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB1
Gene (Uniprot):RPO21
Chain IDs:A
Chain Length:135
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P04050 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB2
Gene (Uniprot):RPB2
Chain IDs:B
Chain Length:102
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P08518 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB3
Gene (Uniprot):RPB3
Chain IDs:C
Chain Length:347
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P16370 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB4
Gene (Uniprot):RPB4
Chain IDs:D
Chain Length:125
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20433 Pfam ID:PF03874
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC1
Gene (Uniprot):RPB5
Chain IDs:E
Chain Length:215
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20434 Pfam ID:PF03871, PF01191
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Gene (Uniprot):RPO26
Chain IDs:F
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20435 Pfam ID:PF01192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
Gene (Uniprot):RPB7
Chain IDs:G
Chain Length:129
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P34087 Pfam ID:PF03876, PF00575
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Gene (Uniprot):RPB8
Chain IDs:H
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P20436 Pfam ID:PF03870
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB9
Gene (Uniprot):RPB9
Chain IDs:I
Chain Length:122
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P27999 Pfam ID:PF02150, PF01096
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Gene (Uniprot):RPB10
Chain IDs:J
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P22139 Pfam ID:PF01194
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB11
Gene (Uniprot):RPB11
Chain IDs:K
Chain Length:120
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P38902 Pfam ID:PF13656
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC4
Gene (Uniprot):RPC10
Chain IDs:L
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40422 Pfam ID:PF03604
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIB
Gene (Uniprot):SUA7
Chain IDs:M
Chain Length:352
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P29055 Pfam ID:PF08271, PF00382
Polymer Type:polydeoxyribonucleotide
Molecule:Non-template DNA (219-MER)
Chain IDs:N
Chain Length:219
Number of Molecules:1
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Molecule:TATA-box-binding protein
Gene (Uniprot):SPT15
Chain IDs:O
Chain Length:247
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P13393 Pfam ID:PF00352
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIF subunit alpha
Gene (Uniprot):TFG1
Chain IDs:P (auth: Q)
Chain Length:738
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41895 Pfam ID:PF05793
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIF subunit beta
Gene (Uniprot):TFG2
Chain IDs:Q (auth: R)
Chain Length:400
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P41896 Pfam ID:PF17683, PF02270
Polymer Type:polydeoxyribonucleotide
Molecule:Template DNA (219-MER)
Chain IDs:R (auth: T)
Chain Length:219
Number of Molecules:1
Biological Source:synthetic construct
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIA large subunit
Chain IDs:S (auth: U)
Chain Length:171
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32773 Pfam ID:PF03153
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIA subunit 2
Gene (Uniprot):TOA2
Chain IDs:T (auth: V)
Chain Length:129
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32774 Pfam ID:PF02268, PF02751
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIE subunit alpha
Gene (Uniprot):TFA1
Chain IDs:U (auth: W)
Chain Length:492
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36100 Pfam ID:PF02002
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIE subunit beta
Gene (Uniprot):TFA2
Chain IDs:V (auth: X)
Chain Length:328
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36145 Pfam ID:PF02186, PF18121, PF22254
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H3.2
Chain IDs:EA (auth: a), IA (auth: e)
Chain Length:135
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P84233 Pfam ID:PF00125
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H4
Chain IDs:FA (auth: b), JA (auth: f)
Chain Length:102
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P62799 Pfam ID:PF15511
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2A
Chain IDs:GA (auth: c), KA (auth: g)
Chain Length:347
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P06897 Pfam ID:PF00125, PF16211
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Histone H2B 1.1
Chain IDs:HA (auth: d), LA (auth: h)
Chain Length:125
Number of Molecules:2
Biological Source:Xenopus laevis
UniProt ID:P02281 Pfam ID:PF00125
Ligand Molecules
MG
SF4
ZN
Primary Citation
Structures of transcription preinitiation complex engaged with the +1 nucleosome.
Nat.Struct.Mol.Biol. 30 226 232 (2023)
PMID: 36411341 DOI: 10.1038/s41594-022-00865-w

Abstact

The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC assembles within chromatin. In the yeast Saccharomyces cerevisiae, PIC assembly occurs adjacent to the +1 nucleosome that is located downstream of the core promoter. Here we present cryo-EM structures of the yeast PIC bound to promoter DNA and the +1 nucleosome located at three different positions. The general transcription factor TFIIH engages with the incoming downstream nucleosome and its translocase subunit Ssl2 (XPB in human TFIIH) drives the rotation of the +1 nucleosome leading to partial detachment of nucleosomal DNA and intimate interactions between TFIIH and the nucleosome. The structures provide insights into how transcription initiation can be influenced by the +1 nucleosome and may explain why the transcription start site is often located roughly 60 base pairs upstream of the dyad of the +1 nucleosome in yeast.

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Chemical

Disease

Primary Citation of related structures
7ZSB